Module 01

Module 01 Portfolio Check

  • Installation check
    • Completion status:
    • Comments:
  • Portfolio repo setup
    • Completion status:
    • Comments:
  • RMarkdown Pretty PDF Challenge
    • Completion status:
    • Comments:
  • Evidence worksheet_01
    • Completion status:
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  • Evidence worksheet_02
    • Completion status:
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  • Evidence worksheet_03
    • Completion status:
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  • Problem Set_01
    • Completion status:
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  • Problem Set_02
    • Completion status:
    • Comments:
  • Writing assessment_01
    • Completion status:
    • Comments:
  • Additional Readings
    • Completion status:
    • Comments:

Data Science Friday

Installation check

Use this space to include your installation screenshots.

Portfolio repo setup

Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.

$ mkdir MICB425_portfolio #make portfolio directory within desired directory
$ cd MICB425_portfolio #go to new directory
$ git init #designate it as a repo
$ touch ID.txt #create blank ID.txt file
$ git add . #stage all files in new repo for commit
$ git commit -m "First commit" #commit files
$ git remote add origin https://github.com/ryankn/MICB425_portfolio #designate remote repo URL
$ git remove -v #verify remote repo URL
$ git push -u origin master #push local repo to remote repo

RMarkdown pretty PDF challenge

Paste your code from the in-class activity of recreating the example PDF.

R Markdown PDF Challenge

The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.

http://phdcomics.com/ Comic posted 1-17-2018

Challenge Goals

The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)

hint: go to the PhD Comics website to see if you can find the image above
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown

Here’s a header!

Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).

Another header, now with maths

Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:

1231521+12341556280987
## [1] 1.234156e+13

Table Time

Or maybe, after you’ve added those numbers, you feel like it’s about time for a table!
I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the future.

library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")
I made this table with kable in the knitr package library
speed dist
Min. : 4.0 Min. : 2.00
1st Qu.:12.0 1st Qu.: 26.00
Median :15.0 Median : 36.00
Mean :15.4 Mean : 42.98
3rd Qu.:19.0 3rd Qu.: 56.00
Max. :25.0 Max. :120.00

And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!

Origins and Earth Systems

Evidence worksheet 01

The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).

As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t want to clutter the Table of Contents too much.

Whitman et al 1998

Learning objectives

Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.

General questions

  • What were the main questions being asked?
    What is the total number of prokaryotes and the total amount of their cellular carbon on earth?

  • What were the primary methodological approaches used?
    To make calculation of such figures more plausible, the number of prokaryotes in three large habitats in which current knowledge suggests most prokaryotes reside in were examined, namely: aquatic environments, soil, and the subsurface. All numbers were used from previously published papers reporting various figures like CFU/mL counts, volume estimations, or C content.

  • Summarize the main results or findings.

  • Do new questions arise from the results?

  • Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?

Problem set 01

Learning objectives:

Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.

Specific questions:

  • What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.

  • What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?

  • What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?

  • Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?

  • Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?

  • Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
    As prokaryotes have been detected at altitudes as high as 57-77 km, it is arguable that that would be the upper boundary of the Earth’s biosphere.

  • How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
    Annual cellular production of prokaryotes was calculated based on literature values for population size and population turnover time in days. In the following example calculation, population size is P, turnover time is T, and annual cellular production is A.

\[A=P*\frac{365}{T}\]

  • What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
    Carbon assimilation efficiency and carbon content determine turnover rates in the upper 200m of the ocean. The amount of net primary productivity required to sustain prokaryotic turnover is dependent on both C assimilation efficiency and total carbon content of the population, which then sets an upper limit on turnover rates. These vary between habitats because different assimilation efficiencies and total carbon content, as well as the amount of total net primary productivity each habitat zone consumes.

  • How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)

  • Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?

  • What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?

Module 01 references

Utilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.

An example for Whitman and Wiebe (1998) has been included below.

Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863